Magnetic tomography is an ill-posed and ill-conditioned inverse problem since, in general, the solution is non-unique and the measured magnetic field is affected by high noise. We use a joint sparsity constraint to regularize the magnetic inverse problem. This leads to a minimization problem whose solution can be approximated by an iterative thresholded Landweber algorithm. The algorithm is proved to be convergent and an error estimate is also given. Numerical tests on a bidimensional problem show that our algorithm outperforms Tikhonov regularization when the measurements are distorted by high noise.